From 08198f79f6bc3f540bc7c2ac431beee571cff43f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 16 May 2019 17:37:48 +0200
Subject: [PATCH] rmi_splitter.py: fix parse_ntuple_fastq to work with Reads
class
---
src/rmi_splitter/rmi_splitter.py | 37 +++++++++++++++++++++-----------
1 file changed, 25 insertions(+), 12 deletions(-)
diff --git a/src/rmi_splitter/rmi_splitter.py b/src/rmi_splitter/rmi_splitter.py
index 8c0abdf..2391e5a 100644
--- a/src/rmi_splitter/rmi_splitter.py
+++ b/src/rmi_splitter/rmi_splitter.py
@@ -589,15 +589,22 @@ def write_seqs(reads_list, fouts, config, sample, verbose=False):
ntuple += 1
-def read_reads(fins, reads_list, ntuple):
+def read_reads(fins, reads_list, ntuple, line_number):
"""
read a read from handle
params: fin file handle
return: read str()
"""
- for reads in ntuple:
- reads_list[reads-1].read(fin=fins[reads-1])
+ if line_number == 0:
+ for reads in ntuple:
+ reads_list[reads-1].header = fins[reads-1]
+ if line_number == 1:
+ for reads in ntuple:
+ reads_list[reads-1].seq = fins[reads-1]
+ if line_number == 3:
+ for reads in ntuple:
+ reads_list[reads-1].str2qual(fins[reads-1])
return reads_list
@@ -616,6 +623,7 @@ def parse_ntuples_fastq(ffastqs,
barcode_dictionary = create_barcode_dictionaries(config=config,
mismatch=mismatch)
sequences_number = 0
+ line_number = 0
reads_list = list()
for read in ntuple:
reads_list.append(Reads())
@@ -624,16 +632,21 @@ def parse_ntuples_fastq(ffastqs,
fins=list_ffastqs,
ntuple=ntuple,
reads_list=reads_list,
+ line_number=line_number,
)
- sample = assign_reads(reads_list=reads_list,
- config=config,
- barcode_dictionary=barcode_dictionary,
- verbose=verbose)
- write_seqs(reads_list=reads_list,
- fouts=fouts,
- config=config,
- sample=sample,
- verbose=verbose)
+ if line_number == 3:
+ sample = assign_reads(reads_list=reads_list,
+ config=config,
+ barcode_dictionary=barcode_dictionary,
+ verbose=verbose)
+ write_seqs(reads_list=reads_list,
+ fouts=fouts,
+ config=config,
+ sample=sample,
+ verbose=verbose)
+ line_number = 0
+ else:
+ line_number += 1
sequences_number += 1
print("number of processed sequences: " +
str(sequences_number-1) +
--
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